Genome-Wide Analysis of Cotton miRNAs During Whitefly Infestation Offers New Insights into Plant-Herbivore Interaction

Insect Resistance: An Emerging Molecular Framework Linking Plant Age and JA Signaling

(2017) Emmanuel Gaquerel et al.   Molecular Plant

Ancient trans -Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response

(2016) Yevgeniy Plavskin et al.   DEVELOPMENTAL CELL

Expression of an insecticidal fern protein in cotton protects against whitefly

(2016) Anoop Kumar Shukla et al.   NATURE BIOTECHNOLOGY

Transcriptome analysis reveals a comprehensive insect resistance response mechanism in cotton to infestation by the phloem feeding insectBemisia tabaci(whitefly)

(2016) Jianying Li et al.   PLANT BIOTECHNOLOGY JOURNAL

miRNA-mediated auxin signalling repression during Vat -mediated aphid resistance in Cucumis melo

(2016) Sampurna Sattar et al.   PLANT CELL AND ENVIRONMENT

A dynamic evolutionary and functional landscape of plant phased small interfering RNAs

(2015) Yi Zheng et al.   BMC BIOLOGY

Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize

(2015) Chunyan Fan et al.   BMC GENOMICS

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypiumspp.)

(2015) Maojun Wang et al.   NEW PHYTOLOGIST

MicroRNA Expression Profile during Aphid Feeding in Chrysanthemum (Chrysanthemum morifolium)

(2015) Xiaolong Xia et al.   PLoS One

PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades

(2014) Qingli Guo et al.   BIOINFORMATICS

Systematic analysis of phloem-feeding insect-induced transcriptional reprogramming in Arabidopsis highlights common features and reveals distinct responses to specialist and generalist insects

(2014) Christine H. Foyer et al.   JOURNAL OF EXPERIMENTAL BOTANY

Differential expression of microRNAs and other small RNAs in barley between water and drought conditions

(2014) Michael Hackenberg et al.   PLANT BIOTECHNOLOGY JOURNAL

MicroRNA profiling analysis throughout tomato fruit development and ripening reveals potential regulatory role of RIN on microRNAs accumulation

(2014) Chao Gao et al.   PLANT BIOTECHNOLOGY JOURNAL

An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes

(2014) Siwaret Arikit et al.   PLANT CELL

Resistance ofArabidopsis thalianato the green peach aphid,Myzus persicae, involves camalexin and is regulated by microRNAs

(2013) Graeme J. Kettles et al.   NEW PHYTOLOGIST

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Identification and profiling of miRNAs during herbivory reveals jasmonate-dependent and -independent patterns of accumulation in Nicotiana attenuata

(2012) Tohir A Bozorov et al.   BMC PLANT BIOLOGY

Cucumis meloMicroRNA Expression Profile During Aphid Herbivory in a Resistant and Susceptible Interaction

(2012) Sampurna Sattar et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

(2012) Andrew H. Paterson et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

A MicroRNA Cascade in Plant Defense

(2012) N. A. Eckardt   PLANT CELL

A convenient method for simultaneous quantification of multiple phytohormones and metabolites: application in study of rice-bacterium interaction

(2012) Hongbo Liu et al.   Plant Methods

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

MicroRNA regulation of plant innate immune receptors

(2012) F. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants

(2011) Xiaozeng Yang et al.   BIOINFORMATICS

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs

(2011) J. Zhai et al.   GENES & DEVELOPMENT

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Pinellia ternata agglutinin expression in chloroplasts confers broad spectrum resistance against aphid, whitefly, Lepidopteran insects, bacterial and viral pathogens

(2011) Shuangxia Jin et al.   PLANT BIOTECHNOLOGY JOURNAL

New Insights into Plant Responses to the Attack from Insect Herbivores

(2010) Jianqiang Wu et al.   Annual Review of Genetics

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

miR390,Arabidopsis TAS3tasiRNAs, and TheirAUXIN RESPONSE FACTORTargets Define an Autoregulatory Network Quantitatively Regulating Lateral Root Growth

(2010) Elena Marin et al.   PLANT CELL

Release of Hormones from Conjugates: Chloroplast Expression of  -Glucosidase Results in Elevated Phytohormone Levels Associated with Significant Increase in Biomass and Protection from Aphids or Whiteflies Conferred by Sucrose Esters

(2010) S. Jin et al.   PLANT PHYSIOLOGY

Mirid Bug Outbreaks in Multiple Crops Correlated with Wide-Scale Adoption of Bt Cotton in China

(2010) Y. Lu et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Small RNAs and Their Roles in Plant Development

(2009) Xuemei Chen   Annual Review of Cell and Developmental Biology

Roles of Plant Small RNAs in Biotic Stress Responses

(2009) Virginia Ruiz-Ferrer et al.   Annual Review of Plant Biology

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173

(2009) Felipe F Felippes et al.   EMBO REPORTS

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

(2008) C. Addo-Quaye et al.   BIOINFORMATICS

Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide

(2008) Shijun Mi et al.   CELL

Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation

(2008) Taiowa A. Montgomery et al.   CELL

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY

Herbivory-induced changes in the small-RNA transcriptome and phytohormone signaling in Nicotiana attenuata

(2008) S. P. Pandey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA